How to make elements of mini cooper (door, hood, fender, bumpers, side panel) and their transitions smooth?
I examined the screen shots, and then examined the blend file, and found immediately what the problem is. The geometry does not match across the joints in the body. I opened your blend file, combined the front fender, door, and rear fender into the same object using CTRL - J, and with the side view selected, switched into edit mode. Here is a screen shot:



Note that in the front fender, you have five segments, and in the rear fender you have seven, but in the door you only have four. To have the meshes line up on either side of the joints, you need to have exactly the same geometry on either side of the joint, so you'll need to add two more segments on the front fender, and three more on the door, and the x and z values of each pair of vertices on either side of a joint along the front and rear door edges will have to be identical, with the only difference being a small variance in the x value of the vertices in each pair. The same will be true of the joints between the fenders and the hood, and between the rear fenders and the rear door. 

If I were doing this model, I'd likely make the door, and two side fenders a single object, and when I had the whole side to my liking, go back, and add a couple of loop cuts to define the front and rear edges of the door.